QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended June 30, 2013

or

¨

TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from
to

Commission File Number: 1-32731

CHIPOTLE
MEXICAN GRILL, INC.

(Exact name of registrant as specified in its charter)

Delaware

84-1219301

(State or other jurisdiction of

incorporation or organization)

(IRS Employer

Identification No.)

1401 Wynkoop St., Suite 500 Denver, CO

80202

(Address of Principal Executive Offices)

(Zip Code)

Registrants telephone number, including area code: (303) 595-4000

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the
Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90
days. x Yes ¨ No

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every
Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such
files). x Yes ¨ No

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller
reporting company. See definitions of large accelerated filer, accelerated filer and smaller reporting company in Rule 12b-2 of the Exchange Act. (Check one):

Large accelerated filer

x

Accelerated filer

¨

Non-accelerated filer

¨ (Do not check if a smaller reporting company)

Smaller reporting company

¨

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the
Exchange Act). ¨ Yes x No

As of July 15, 2013 there were 30,869,464 shares of the registrants common stock, par value of $0.01 per share outstanding.

Chipotle Mexican Grill, Inc. (the Company), a Delaware corporation, develops and operates fast-casual,
fresh Mexican food restaurants throughout the United States. The Company also has five restaurants in Canada, six in London, England, and one in Paris, France. As of June 30, 2013, the Company operated 1,502 restaurants, including two ShopHouse
Southeast Asian Kitchen restaurants. The Company manages its operations based on seven regions and has aggregated its operations to one reportable segment.

The accompanying unaudited condensed consolidated financial statements of the Company have been prepared in accordance with U.S. generally accepted accounting principles for interim financial statements
and pursuant to the rules and regulations of the Securities and Exchange Commission. In the opinion of management, the accompanying unaudited condensed consolidated financial statements reflect all adjustments consisting of normal recurring
adjustments necessary for a fair presentation of its financial position and results of operations. Interim results of operations are not necessarily indicative of the results that may be achieved for the full year. The financial statements and
related notes do not include all information and footnotes required by U.S. generally accepted accounting principles for annual reports. This quarterly report should be read in conjunction with the consolidated financial statements included in the
Companys annual report on Form 10-K for the year ended December 31, 2012.

Certain amounts in prior periods have
been reclassified to conform to the current year presentation. During the first quarter of 2013, the Company reclassified amounts related to lease financing liabilities from deemed landlord financing to other liabilities, and from current portion of
deemed landlord financing to accrued liabilities. Such reclassifications did not have a material effect on the Companys consolidated financial position or results of operations.

The Company has evaluated subsequent events and transactions for potential recognition or disclosure in the financial statements through
the day the financial statements are issued.

2. Adoption of New Accounting Principles

Effective January 1, 2013, the Company adopted Accounting Standards Update (ASU) No. 2013-02,
Reporting of Amounts Reclassified Out of Accumulated Other Comprehensive Income. The adoption of ASU 2013-02 concerns presentation and disclosure only and did not have an impact on the Companys consolidated financial position or
results of operations.

3. Fair Value of Financial Instruments

The carrying value of the Companys cash and cash equivalents, accounts receivable and accounts payable
approximate fair value because of their short-term nature. Investments, all of which are classified as held-to-maturity, are carried at amortized cost, which approximates fair value. Investments consist of U.S. treasury notes and CDARS, certificates
of deposit placed through an account registry service, with maturities up to approximately two years. Fair market value of U.S. treasury notes is measured using level 1 inputs (quoted prices for identical assets in active markets) and fair market
value of CDARS is measured based on level 2 inputs (quoted prices for identical assets in markets that are not active).

The
Company also maintains a rabbi trust to fund obligations under a deferred compensation plan. Amounts in the rabbi trust are invested in mutual funds, which are designated as trading securities and carried at fair value, and are included in other
assets in the consolidated balance sheet. Fair market value of mutual funds is measured using level 1 inputs (quoted prices for identical assets in active markets). The fair value of the investments in the rabbi trust was $12,091 and $10,037 as of
June 30, 2013 and December 31, 2012, respectively. The Company records trading gains and losses in general and administrative expenses in the consolidated statement of income, along with the offsetting amount related to the increase or
decrease in deferred compensation to reflect its exposure of the deferred plan liability. The Company recorded $147 of unrealized losses on investments held in the rabbi trust during the three months ended June 30, 2013, and $138 of unrealized
gains on investments held in the rabbi trust during the six months ended June 30, 2013. The Company recorded $292 and $91 of unrealized losses on investments held in the rabbi trust during the three and six months ended June 30, 2012,
respectively.

4. Income Taxes

In January 2013, the United States Congress authorized, and the President signed into law, certain federal tax credits
that will be reflected in the Companys U.S. tax return for 2012. However, since the law was enacted in 2013, the financial statement benefit of such credits totaling $3,275 was reflected in the provision for income taxes in the consolidated
statement of income and comprehensive income during the first quarter of 2013.

The Company has announced authorizations by its Board of Directors of repurchases of shares of common stock, which in
the aggregate authorized expenditures of up to $700,000. Under the remaining repurchase authorizations, shares may be purchased from time to time in open market transactions, subject to market conditions.

On November 20, 2012 the Company entered into a privately negotiated accelerated share repurchase transaction (ASR) to
repurchase $25,000 of its common stock. The Company advanced $25,000 on November 20, 2012 and received 65 shares, which represented 70% of the total number of shares to be repurchased calculated using the closing price on November 20,
2012. The agreement was settled in February 2013, and the Company received an additional 22 shares, resulting in a weighted-average price per share of $287.20 for the ASR.

During the six months ended June 30, 2013 the shares of common stock repurchased under authorized programs, including the ASR, was
270 for a total cost of $80,612. The cumulative shares repurchased under authorized programs as of June 30, 2013 are 3,993 for a total cost of $580,715. As of June 30, 2013, $119,575 was available to repurchase shares under the current
repurchase authorization. The shares are being held in treasury stock until such time as they are reissued or retired at the discretion of the Board of Directors.

6. Stock-based Compensation

During the first quarter of 2013, the Company granted stock only stock appreciation rights (SOSARs) on 662
shares of its common stock to eligible employees, of which 191 include performance conditions. The grant date fair value of the SOSARs was $82.03 per share with an exercise price of $318.45 per share based on the closing price of common stock on the
date of grant. The SOSARs (other than those subject to performance conditions) vest in two equal installments on the second and third anniversary of the grant date.

Total stock-based compensation expense was $19,243 and $34,898 ($11,704 and $21,225 net of tax) for the three and six months ended June 30, 2013, respectively, and was $18,045 and $38,805 ($11,004
and $23,663 net of tax) for the three and six months ended June 30, 2012, respectively. A portion of stock-based compensation totaling $297 and $565 for the three and six months ended June 30, 2013, and $608 and $1,128 for the three and
six months ended June 30, 2012, was recognized as capitalized development and is included in leasehold improvements, property and equipment in the consolidated balance sheet. During the six months ended June 30, 2013, 93 options or SOSARs
were exercised, 42 SOSARs were forfeited, and 6 non-vested stock awards vested.

7. Earnings Per Share

Basic earnings per share is calculated by dividing income available to common shareholders by the weighted-average
number of shares of common stock outstanding during each period. Diluted earnings per share (diluted EPS) is calculated using income available to common shareholders divided by diluted weighted-average shares of common stock outstanding
during each period. Potentially dilutive securities include common shares related to stock options, SOSARs and non-vested stock awards (collectively stock awards). For the three and six months ended June 30, 2013, 883 and 781 stock
awards were excluded from the calculation of diluted EPS, and for the three and six months ended June 30, 2012, 365 and 311 stock awards, were excluded from the calculation of diluted EPS because they were anti-dilutive. In addition, 437 and
473 stock awards for the three and six months ended June 30, 2013 and 492 and 454 stock awards for the three and six months ended June 30, 2012 were excluded from the calculation of diluted EPS because they were subject to performance
conditions.

The following table sets forth the computations of basic and diluted earnings per share:

Notices of Inspection of Work Authorization Documents and Related Civil and Criminal Investigations

Following an inspection during 2010 by the U.S. Department of Homeland Security, or DHS, of the work authorization documents of the
Companys restaurant employees in Minnesota, the Immigration and Customs Enforcement arm of DHS, or ICE, issued to the Company a Notice of Suspect Documents identifying a large number of employees who, according to ICE and notwithstanding the
Companys review of work authorization documents for each employee at the time they were hired, appeared not to be authorized to work in the U.S. The Company approached each of the named employees to explain ICEs determination and
afforded each employee an opportunity to confirm the validity of their original work eligibility documents, or provide valid work eligibility documents. Employees who were unable to provide valid work eligibility documents were terminated in
accordance with the law. In December 2010, the Company was also requested by DHS to provide the work authorization documents of restaurant employees in the District of Columbia and Virginia, and the Company provided the requested documents in
January 2011, and subsequently received additional requests for work authorization documents covering a small number of individual restaurants as well. In April 2011, the Company also received notice from the office of the U.S. Attorney for the
District of Columbia that it is conducting an investigation into these matters through its criminal division. In April 2013 the civil division of the U.S. Attorneys Office for the District of Columbia requested work authorization documents for
all of the Companys employees since 2007, plus employee lists and other documents concerning work authorization. The Company believes its practices with regard to the work authorization of its employees, including the review and retention of
work authorization documents, are in compliance with applicable law. However, the termination of large numbers of employees in a short period of time does disrupt restaurant operations and results in a temporary increase in labor costs as new
employees are trained.

In May 2012, the U.S. Securities and Exchange Commission notified the Company that it is conducting a
civil investigation of the Companys compliance with employee work authorization verification requirements and its related disclosures and statements, and the office of the U.S. Attorney for the District of Columbia advised the Company that its
investigation has broadened to include a parallel criminal and civil investigation of the Companys compliance with federal securities laws. The Company intends to continue to fully cooperate in the governments investigations. It is not
possible at this time to determine whether the Company will incur any fines, penalties or further liabilities in connection with these matters.

Shareholder Derivative Actions

On July 12, 2012, Ralph B. Richey
filed a shareholder derivative action in the U.S. District Court for the District of Colorado alleging that the members of the Companys Board of Directors breached their fiduciary duties in connection with employee work authorization
compliance matters. On September 21, 2012, Joanne Nelson filed a shareholder derivative action in the same court alleging that the members of the Companys Board of Directors and the Companys Chief Financial Officer breached their
fiduciary duties, caused waste of corporate assets, and were unjustly enriched in connection with employee work authorization compliance matters, as well as in connection with the Companys alleged failure to disclose material information about
the Companys business results and prospects, and in connection with compensation paid to some of the Companys officers. On October 4, 2012, Francis Schmitz filed a shareholder derivative action in the same court, making allegations
substantially the same as those in the Nelson complaint. Each of these actions purports to state a claim for damages on behalf of the Company, and is based on statements in the Companys SEC filings and related public disclosures, as well as
media reports and Company records, in part regarding the matters described above under -Notices of Inspection of Work Authorization Documents and Related Civil and Criminal Investigations. On January 17, 2013, these
three shareholder derivative actions were consolidated by the court and will proceed as a single action. On March 20, 2013, an amended and consolidated complaint for the cases was filed by plaintiff Saleem Mohammed. On May 22, 2013, the
Company filed a motion to dismiss the consolidated cases, and a ruling on the motion remains pending. The Company intends to defend the cases vigorously, but it is not possible at this time to reasonably estimate the outcome of or any potential
liability from these cases.

Shareholder Class Actions

On August 16, 2012, City of Dania Beach Police & Firefighters Retirement System filed a complaint in the U.S. District Court
for the District of Colorado on behalf of a purported class of purchasers of shares of the Companys common stock between February 1, 2012 and July 19, 2012. On August 17, 2012, Sonia Kim filed a complaint in the U.S. District
Court for the District of Colorado that was otherwise identical to the City of Dania Beach Police & Firefighters complaint. The complaints purported to state claims against the Company, each of its co-Chief Executive Officers and its Chief
Financial Officer under Sections 10(b) and 20(a) of the Exchange Act and related rules and regulations, based on the Companys alleged failure during the claimed class period to disclose material information about the Companys business
results and prospects. The lead plaintiff in the consolidated actions determined not to pursue the case, and joined with the Company in filing a stipulated dismissal of the case on July 3, 2013. As a result, these actions were terminated
without any findings of liability or other adverse determinations related to the Company, its disclosures or any of its officers, and without any liability other than each partys liability for its own attorneys fees and costs.

The Company is involved in various other claims and legal actions that arise in the ordinary course of business. The Company does not
believe that the ultimate resolution of these actions will have a material adverse effect on the Companys financial position, results of operations, liquidity or capital resources. However, a significant increase in the number of these claims,
or one or more successful claims under which the Company incurs greater liabilities than the Company currently anticipates, could materially and adversely affect the Companys business, financial condition, results of operations and cash flows.

MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Cautionary Note Regarding Forward-Looking Statements

Certain statements in this
report, including projections of the number and type of restaurants we intend to open, potential changes in comparable restaurant sales, statements regarding possible menu price increases, projections of food cost trends and marketing spending,
discussion of possible stock repurchases, and estimates of our effective tax rates, are forward-looking statements as defined in the Private Securities Litigation Reform Act of 1995. We use words such as anticipate, believe,
could, should, estimate, expect, intend, may, predict, project, target, and similar terms and phrases, including references to assumptions,
to identify forward-looking statements. These forward-looking statements are based on information available to us as of the date any such statements are made, and we assume no obligation to update these forward-looking statements. These statements
are subject to risks and uncertainties that could cause actual results to differ materially from those described in the statements. These risks and uncertainties include, but are not limited to, the risk factors described in our annual report on
Form 10-K for the year ended December 31, 2012, as updated in Part II, Item 1.A of this report.

Overview

Chipotle operates fresh Mexican food restaurants serving burritos, tacos, burrito bowls (a burrito without the tortilla)
and salads. We began with a simple philosophy: demonstrate that food served fast doesnt have to be a traditional fast-food experience. We do this by avoiding a formulaic approach when creating our restaurant experience, looking to
fine dining restaurants for inspiration. We use high-quality raw ingredients, classic cooking methods and distinctive interior design, and have friendly people to take care of each customerfeatures that are more frequently found in the world
of fine dining. Our approach is also guided by our belief in an idea we call Food With Integrity. Our objective is to find the highest quality ingredients we caningredients that are grown or raised with respect for the environment,
animals and people who grow or raise the food. A similarly focused people culture, with an emphasis on identifying and empowering top performing employees, enables us to develop future leaders from within.

2013 Highlights

Restaurant Development. As of June 30, 2013, we had 1,502 restaurants, of which 1,490 were located throughout the United States, five in Canada, six in London, England, and one in Paris,
France. Our restaurants include two ShopHouse Southeast Asian Kitchen restaurants, our new concept serving Asian inspired cuisine. New restaurants have contributed substantially to our revenue growth. We opened 92 restaurants during the six months
ended June 30, 2013. We expect to open 165 to 180 restaurants in 2013, including up to four additional ShopHouse restaurants.

Sales Growth. Average restaurant sales were $2.119 million as of June 30, 2013. We define average restaurant sales as the average trailing 12-month sales for restaurants in operation for at
least 12 full calendar months. Our comparable restaurant sales increased 3.4% for the first six months of 2013, and 5.5% for the second quarter of 2013. Comparable restaurant sales represent the change in period-over-period sales for
restaurants beginning in their 13th full month of operation. Comparable restaurant sales increases in the first six months of 2013 were driven primarily by an increase in customer visits; and comparable restaurant sales increases for the second
quarter of 2013 were driven primarily by an increase in customer visits and one additional day of sales as Easter fell in the first quarter of 2013, instead of the second quarter as in 2012. Taking into account our recent transaction trends, we
expect our full year comparable restaurant sales increases in 2013 to be in the low to mid-single digits.

During the first
half of 2013, we launched our catering service in select markets, and we expect to offer catering in all of our Chipotle restaurants in the U.S. by the end of the year.

Food With Integrity. In all of our restaurants, we endeavor to serve only meats that were raised without the use of subtherapeutic antibiotics or added hormones, and in accordance with criteria
weve established in an effort to improve sustainability and promote animal welfare. In addition, a portion of some of the produce items we serve is organically grown, or sourced locally when in season (by which we mean within 350 miles of
our restaurant), and a portion of the beans we serve is organically grown and a portion is grown using conservation tillage methods that improve soil conditions, reduce erosion and help preserve the environment in which they are grown. The sour
cream and cheese we buy is made with milk that comes from cows that are not given rBGH. Milk used to make much of our cheese and sour cream is sourced from dairies that provide an even higher standard of animal welfare by providing outdoor access
for their cows. We will continue to search for quality ingredients that not only taste delicious, but also benefit local farmers or the environment, or otherwise benefit or improve the sustainability of our supply chain.

One of our primary goals is for all of our restaurants to continue serving meats that are raised to meet our standards, but we have and
will continue to face challenges in doing so. Some of our restaurants served conventionally raised beef and chicken for periods during the first half of 2013 and some are continuing to serve conventionally raised beef, and more of our restaurants
may periodically serve conventionally raised meats in the future due to additional supply constraints. When we become aware that one or more of our restaurants will serve conventionally raised meat, we clearly and specifically disclose this
temporary change on signage in each affected restaurant, so that customers can avoid those meats if they choose to do so.

Our
food costs increased as a percentage of revenue for the first six months of 2013 as compared to 2012 as a result of inflationary pressures on many of our ingredients, particularly salsa ingredients due in part to tomatillo shortages in Mexico, as
well as dairy and chicken, partially offset by relief in avocado prices, as well as the impact of purchasing more conventionally raised beef. We expect that food cost inflation will continue in 2013 and that our food costs as a percentage of revenue
will increase modestly.

Stock Repurchases. In accordance with stock repurchases authorized by our Board of
Directors we purchased stock with an aggregate total repurchase price of $80.6 million during the first six months of 2013. As of June 30, 2013, $119.6 million was available to be repurchased under the current repurchase authorizations. We have
entered into an agreement with a broker under SEC rule 10b5-1(c), authorizing the broker to make open market purchases of common stock from time to time, subject to market conditions. The existing repurchase agreement and the Boards
authorization of the repurchases may be modified, suspended, or discontinued at any time.

Restaurant Activity

The following table details restaurant unit data for the periods indicated.

For the three monthsended June 30

For the six monthsended June 30

2013

2012

2013

2012

Beginning of period

1,458

1,262

1,410

1,230

Openings

44

55

92

87

Relocations



(1

)



(1

)

Total restaurants at end of period

1,502

1,316

1,502

1,316

Results of Operations

Our results of operations as a percentage of revenue and period-over-period variances are discussed in the following section. As our business grows and we open more restaurants and hire more employees,
our aggregate restaurant operating costs increase.

Revenue

For the three monthsended June 30

%increase

For the six monthsended June 30

%increase

2013

2012

2013

2012

(dollars in millions)

Revenue

$

816.8

$

690.9

18.2

%

$

1,543.5

$

1,331.5

15.9

%

Average restaurant sales

$

2.119

$

2.106

0.6

%

$

2.119

$

2.106

0.6

%

Comparable restaurant sales increases

5.5

%

8.0

%

3.4

%

10.2

%

Number of restaurants as of the end of the period

1,502

1,316

14.1

%

1,502

1,316

14.1

%

Number of restaurants opened in the period, net of relocations

44

54

92

86

The significant factors contributing to our increase in revenue were new restaurant openings and
comparable restaurant sales increases. Revenue for the three and six months ended June 30, 2013 from restaurants not in the comparable restaurant base contributed $88.7 million and $169.5 million of the increase in sales, respectively, of which
$29.1 million and $40.6 million was attributable to restaurants opened in 2013. Comparable restaurant sales increases contributed $37.2 million of the increase in sales for the second quarter of 2013, and $42.8 million of the increase in sales for
the first half of 2013. Comparable restaurant sales growth for the first half of 2013 was primarily due to increases in customer visits.

Food, beverage and packaging costs increased as a percentage of revenue for the three and six months
ended June 30, 2013 as a result of inflation on many of our food items, particularly salsa ingredients due in part to tomatillo shortages in Mexico, as well as dairy and chicken, partially offset by relief in avocado prices, as well as the
impact of purchasing more conventionally raised beef.

Labor Costs

For the three monthsended June 30

%increase

For the six monthsended June 30

%increase

2013

2012

2013

2012

(dollars in millions)

Labor costs

$

185.8

$

159.9

16.2

%

$

357.3

$

311.9

14.6

%

As a percentage of revenue

22.7

%

23.1

%

23.1

%

23.4

%

Labor costs as a percentage of revenue decreased in the three and six months ended June 30, 2013
primarily due to higher average restaurant sales and improvements in staffing leading to lower overtime hours.

Occupancy Costs

For the three monthsended June 30

%increase

For the six monthsended June 30

%increase

2013

2012

2013

2012

(dollars in millions)

Occupancy costs

$

48.6

$

41.8

16.3

%

$

96.2

$

82.3

16.9

%

As a percentage of revenue

5.9

%

6.0

%

6.2

%

6.2

%

Occupancy costs as a percentage of revenue remained relatively consistent in the three and six months
ended June 30, 2013.

Other Operating Costs

For the three monthsended June 30

%increase

For the six monthsended June 30

%increase

2013

2012

2013

2012

(dollars in millions)

Other operating costs

$

86.3

$

66.4

30.1

%

$

163.0

$

132.5

23.0

%

As a percentage of revenue

10.6

%

9.6

%

10.6

%

10.0

%

Other operating costs include, among other items, marketing and promotional costs, bank and credit card
fees, and restaurant utilities and maintenance costs. Other operating costs increased as a percentage of revenue in the three and six months ended June 30, 2013 due primarily to higher spend on marketing and promotion.

The increase in general and administrative expenses in dollar terms in the three months ended
June 30, 2013 primarily resulted from increased payroll and bonus costs as we grew, increased legal costs, and increased non-cash stock-based compensation expense.

The increase in general and administrative expenses in dollar terms in the six months ended June 30, 2013 primarily resulted from increased payroll and bonus costs as we grew, and increased legal
costs. These increases were offset by a decrease in non-cash stock-based compensation expense due to expenses in the first half of 2012 related to non-vested stock awards subject to performance conditions, as well as from a decrease in the employer
portion of taxes paid, primarily from fewer stock award exercises and vesting during 2013 as compared to 2012.

Depreciation and
Amortization

For the three monthsended June 30

%increase

For the six monthsended June 30

%increase

2013

2012

2013

2012

(dollars in millions)

Depreciation and amortization

$

23.6

$

20.5

14.9

%

$

46.5

$

40.6

14.5

%

As a percentage of revenue

2.9

%

3.0

%

3.0

%

3.1

%

The increase in depreciation and amortization in dollar terms was primarily due to restaurants opened in
2013 and 2012. Depreciation and amortization remained relatively consistent as a percentage of revenue.

Provision for Income Taxes

For the three monthsended June 30

%increase

For the six monthsended June 30

%increase

2013

2012

2013

2012

(dollars in millions)

Provision for income taxes

$

58.9

$

52.5

12.2

%

$

102.6

$

92.5

11.0

%

Effective tax rate

40.1

%

39.1

%

38.4

%

39.0

%

We expect our 2013 estimated annual effective tax to be 38.9% compared to 39.3% for 2012. Congress
extended certain tax credits in January 2013 that impacted the 2013 annual effective tax rate favorably by 1.1%. The favorable annual tax rate impact includes 0.6% related to the estimated federal tax credit benefit in 2012 and 0.5% related to the
estimated federal tax credit benefit in 2013. These benefits were partially offset by non-recurring adjustments related to state income taxes in the second quarter, as well as a higher estimated state tax rate.

Seasonality

Seasonal
factors cause our profitability to fluctuate from quarter to quarter. Historically, our average daily restaurant sales and net income are lower in the first and fourth quarters due, in part, to the holiday season and because fewer people eat out
during periods of inclement weather (the winter months) than during periods of mild or warm weather (the spring, summer and fall months). Other factors also have a seasonal effect on our results. For example, restaurants located near colleges and
universities generally do more business during the academic year. The number of trading days can also affect our results. Overall, on an annual basis, changes in trading days do not have a significant impact on our results.

Our quarterly results are also affected by other factors such as the number of new
restaurants opened in a quarter, timing of marketing and promotional spend and both planned and unanticipated events. New restaurants typically have lower margins following opening as a result of the expenses associated with opening new restaurants
and their operating inefficiencies in the months immediately following opening. Accordingly, results for a particular quarter are not necessarily indicative of results to be expected for any other quarter or for any year.

Liquidity and Capital Resources

Our primary liquidity and capital requirements are for new restaurant construction, working capital and general corporate needs. We have a cash and investment balance of $774.1 million that we expect to
utilize, along with cash flow from operations, to provide capital to support the growth of our business (primarily through opening restaurants), to repurchase, as currently authorized, additional shares of our common stock subject to market
conditions, to continue to maintain our existing restaurants and for general corporate purposes. We believe that cash from operations, together with our cash and investment balance, will be enough to meet ongoing capital expenditures, working
capital requirements and other cash needs for the foreseeable future.

We havent required significant working capital
because customers pay using cash or credit cards and because our operations do not require significant receivables, nor do they require significant inventories due, in part, to our use of various fresh ingredients. In addition, we generally have the
right to pay for the purchase of food, beverage and supplies some time after the receipt of those items, generally within ten days, thereby reducing the need for incremental working capital to support growth.

Off-Balance Sheet Arrangements

As of June 30, 2013 we had no off-balance sheet arrangements or obligations.

Critical
Accounting Estimates

Critical accounting estimates are those that we believe are both significant and that require us to
make difficult, subjective or complex judgments, often because we need to estimate the effect of inherently uncertain matters. We base our estimates and judgments on historical experiences and various other factors that we believe to be appropriate
under the circumstances. Actual results may differ from these estimates, and we might obtain different estimates if we used different assumptions or conditions. We had no significant changes in our critical accounting estimates since our last annual
report. Our critical accounting estimates are identified and described in our annual report on Form 10-K for the year ended December 31, 2012.

ITEM 3.

QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Changing Interest Rates

Were exposed to interest rate risk through
fluctuations of interest rates on our investments. Changes in interest rates affect the interest income we earn, and therefore impact our cash flows and results of operations. As of June 30, 2013, we had $572.5 million in investments and
interest-bearing cash accounts, including insurance related restricted trust accounts classified in other assets, and $181.2 million in accounts with an earnings credit we classify as interest income, which combined bear a weighted-average interest
rate of 0.32%.

Commodity Price Risks

We are also exposed to commodity price risks. Many of the ingredients we use to prepare our food, as well as our packaging materials, are commodities or ingredients that are affected by the price of other
commodities, exchange rates, foreign demand, weather, seasonality, production, availability and other factors outside our control. We work closely with our suppliers and use a mix of forward pricing protocols under which we agree with our supplier
on fixed prices for deliveries at some time in the future, fixed pricing protocols under which we agree on a fixed price with our supplier for the duration of that protocol, and formula pricing protocols under which the prices we pay are based on a
specified formula related to the prices of the goods, such as spot prices. However, a portion of the dollar value of goods purchased by us is effectively at spot prices. Generally our pricing protocols with suppliers can remain in effect for periods
ranging from one to 18 months, depending on the outlook for prices of the particular ingredient. In several cases, we have minimum purchase obligations. Weve tried to increase, where necessary, the number of suppliers for our ingredients,
which we believe can help mitigate pricing volatility, and we follow industry news, trade issues, exchange rates, foreign demand, weather, crises and other world events that may affect our ingredient prices. Increases in ingredient prices could
adversely affect our results if we choose not to increase menu prices at the same pace for competitive or other reasons.

Foreign Currency
Exchange Risk

A portion of our operations consists of activities outside of the U.S. and we have currency risk on the
transactions in other currencies and translation adjustments resulting from the conversion of our international financial results into the U.S. dollar. However, a substantial majority of our operations and investment activities are transacted in the
U.S. and therefore our foreign currency risk is limited at this date.

We maintain disclosure controls and procedures (as defined in Rule 13a-15(e) promulgated under the Securities Exchange Act of
1934, as amended (the Exchange Act)) that are designed to ensure that information required to be disclosed in Exchange Act reports is recorded, processed, summarized and reported within the time periods specified in the Securities and
Exchange Commissions rules and forms, and that such information is accumulated and communicated to our management, including our Co-Chief Executive Officers and Chief Financial Officer, as appropriate, to allow timely decisions regarding
required disclosure.

As of June 30, 2013, we carried out an evaluation, under the supervision and with the participation
of our management, including our Co-Chief Executive Officers and Chief Financial Officer, of the effectiveness of the design and operation of our disclosure controls and procedures. Based on the foregoing, our Co-Chief Executive Officers and Chief
Financial Officer concluded that our disclosure controls and procedures were effective as of the end of the period covered by this report.

There were no changes during the three months ended June 30, 2013 in our internal control over financial reporting (as defined in Rule 13a-15(f) under the Exchange Act) that have materially
affected or are reasonably likely to materially affect our internal control over financial reporting.

Shares were repurchased pursuant to a repurchase program announced on November 20, 2012. Repurchases under the program are limited to $100 million in total
repurchase price, and there is no expiration date. Authorization of the ongoing repurchase program may be modified, suspended, or discontinued at any time.

(2)

This column reflects an additional $100 million in authorized repurchases announced on February 5, 2013. Authorization of the repurchase program may be modified,
suspended, or discontinued at any time.

(3)

Includes 1,256 shares of common stock that were surrendered by participants under the Amended and Restated Chipotle Mexican Grill, Inc. 2006 Stock Incentive Plan as
payment of applicable tax withholding on the vesting of shares of restricted stock units. Shares surrendered by the participants pursuant to the terms of that plan and the applicable award agreements are deemed repurchased by us, but are not part of
publicly announced share repurchase programs.

The following financial statements, formatted in XBRL: (i) Condensed Consolidated Balance Sheet as of June 30, 2013 and December 31, 2012, (ii) Condensed Consolidated
Statement of Income and Comprehensive Income for the three and six months ended June 30, 2013 (iii) Condensed Consolidated Statement of Cash Flows for the six months ended June 30, 2013; and (iv) Notes to the Condensed Consolidated
Financial Statements.

*

Incorporated by reference to Chipotle Mexican Grill, Inc.s Registration Statement on Form 8-A/A filed with the Securities and Exchange Commission on
December 16, 2009 (File No. 001-32731).

**

Incorporated by reference to Chipotle Mexican Grill, Inc.s Current Report on Form 8-K filed on January 5, 2009 (File No. 001-32731).

16

EX-3.2

Exhibit 3.2

CERTIFICATE OF AMENDMENT

OF

AMENDED AND RESTATED CERTIFICATE OF INCORPORATION

OF

CHIPOTLE MEXICAN GRILL, INC.

Pursuant to Section 242 of the General Corporation Law of the State of Delaware (the DGCL), Chipotle Mexican
Grill, Inc., a corporation organized and existing under and by virtue of the DGCL (the Corporation), has adopted the following Certificate of Amendment to its Amended and Restated Certificate of Incorporation (the
Certificate of Amendment):

1. The name of the Corporation is Chipotle Mexican Grill, Inc.

2. The following amendments (collectively, the Amendment) to the Amended and Restated Certificate of Incorporation of
the Corporation (the Certificate of Incorporation) were duly adopted by resolution of the Board of Directors of the Corporation on March 14, 2013. The Amendment was adopted by the shareholders of the Corporation at a meeting
of the shareholders duly called and held on May 17, 2013.

3. The Certificate of Incorporation is hereby amended by
deleting Section 1 of Article V and inserting in lieu thereof a new Section 1 of Article V to read as follows:

Section 1.Number. The business and affairs of the Corporation shall be managed
by or under the direction of a Board
of Directors consisting of not fewer than three nor more than 20 directors (exclusive of directors referred to in the last paragraph of this Section 1), the exact number of directors to be determined from time to time by resolution adopted by
the affirmative vote of a majority of the total number of directors then in office.

From the filing and effectiveness of this
Certificate of Amendment with the Secretary of State of the State of Delaware (the Effective Time) until the election of directors at the 2014 annual meeting of shareholders (each annual meeting of shareholders, an Annual
Meeting), pursuant to Section 141(d) of the DGCL, the Board shall be divided into three classes of directors, Class I, Class II and Class III (each class as nearly equal in number as possible), with the directors in Class I having a term
expiring at the 2015 Annual Meeting, the directors in Class II having a term expiring at the 2016 Annual Meeting and the directors in Class III having a term expiring at the 2014 Annual Meeting.

Commencing with the election of directors at the 2014 Annual Meeting, pursuant to Section 141(d) of the DGCL, the Board shall be
divided into two classes of directors, Class I and Class II, with the directors in Class I having a term that expires at the 2015 Annual Meeting and the directors in Class II having a term that expires at the 2016 Annual Meeting. The successors of
the directors who, immediately prior to the 2014 Annual Meeting, were members of Class III (and whose terms expire at the 2014 Annual Meeting) shall be elected to Class I; the directors who, immediately prior to the 2014 Annual Meeting, were members
of Class I (and whose terms were scheduled to expire at the 2015 Annual Meeting) shall become members of Class I for a term expiring at the 2015 Annual Meeting; and the directors who, immediately prior to the 2014 Annual Meeting, were members of
Class II (and whose terms were scheduled to expire at the 2016 Annual Meeting) shall be members of Class II for a term expiring at the 2016 Annual Meeting.

Commencing with the election of directors at the 2015 Annual Meeting, pursuant to
Section 141(d) of the DGCL, there shall be a single class of directors, Class I, with all directors of such class having a term that expires at the 2016 Annual Meeting. The successors of the directors who, immediately prior to the 2015 Annual
Meeting, were members of Class I (and whose terms expire at the 2015 Annual Meeting) shall be elected to Class I and the directors who, immediately prior to the 2015 Annual Meeting, were members of Class II (and whose terms were scheduled to expire
at the 2016 Annual Meeting) shall become members of Class I for a term expiring at the 2016 Annual Meeting.

From and after
the election of directors at the 2016 Annual Meeting, the Board shall cease to be classified as provided in Section 141(d) of the DGCL, and the directors elected at the 2016 Annual Meeting (and each Annual Meeting thereafter) shall be elected
for a term expiring at the next Annual Meeting.

Any additional director of any class elected to fill a vacancy resulting from
an increase in such class shall hold office for the remaining term of that class, but in no case shall a decrease in the number of directors shorten the term of any incumbent director.

Each director shall hold office until the annual meeting for the year in which his or her term expires and until his or her successor
shall be elected and shall qualify, subject, however, to prior death, resignation, retirement, disqualification or removal from office. Directors shall be elected by the affirmative vote of a plurality of the votes cast by shares entitled to vote in
the election at a meeting at which a quorum is present.

Elections of directors at an annual or special meeting of
shareholders shall be by written ballot.

Notwithstanding the foregoing, whenever the holders of any one or more classes or
series of Preferred Stock issued by the Corporation shall have the right, voting separately by class or series, to elect directors at an annual or special meeting of shareholders, the number of such directors and the election, term of office,
filling of vacancies and other features of such directorships shall be governed by the provisions of Article V of this Certificate of Incorporation and any resolution or resolutions adopted by the Board of Directors pursuant thereto, and such
directors shall not be divided into classes unless expressly so provided therein.

4. The Certificate of Incorporation
is hereby amended by deleting Section 3 of Article V and inserting in lieu thereof a new Section 3 of Article V to read as follows:

Until the 2016 Annual Meeting, any director or the entire Board may be removed from office at any time, but only for cause and only by the affirmative vote of the holders of not less than 66 2/3% of
the voting power of the outstanding Common Stock. From and after the election of directors at the 2016 Annual Meeting, any director or the entire Board may be removed from office at any time, with or without cause, but only by the affirmative vote
of the holders of not less than 66 2/3% of the voting power of the outstanding Common Stock.

IN WITNESS WHEREOF, the undersigned has executed this Certificate of Amendment on this 17th
day of May, 2013.

CHIPOTLE MEXICAN GRILL, INC.

By:

/s/ Montgomery Moran

Name:

Montgomery Moran

Title:

Co-Chief Executive Officer and Secretary

EX-10.1

Exhibit 10.1

CHIPOTLE MEXICAN GRILL, INC.

2014 CASH INCENTIVE PLAN

Section 1.

Purpose.

The purpose of
the 2014 Cash Incentive Plan (the Plan) is to promote the interests of Chipotle Mexican Grill, Inc. (Chipotle) and its subsidiaries (collectively the Company) by providing eligible key
employees of the Company with incentive to assist the Company in meeting and exceeding its business goals. The Plan provides opportunities for Participants (as defined in Section 3 below) to earn financial rewards for their role in
assisting Chipotle to meet its annual performance targets. Awards (as defined in Section 5 below) under the Plan are based on the Company achieving the Performance Goal (as defined in Section 5). The Plan will cover each
fiscal year of Chipotle beginning with its 2014 fiscal year. Each such fiscal year is referred to herein as a Performance Period.

Section 2.

Administration.

(a) The
Plan shall be administered by the Executive Compensation Committee (the Committee) of the Board of Directors of Chipotle (the Board) from among its members and shall be comprised of not fewer than two members
who are intended to qualify as outside directors within the
meaning of Section 162(m) of the Internal Revenue Code of 1986, as amended (the Code), and the regulations thereunder.

(b) The Committee shall have broad authority to grant and administer Awards under the Plan and may, subject to the provisions of the
Plan, establish, adopt or revise rules and regulations relating to the Plan or take such actions as it deems necessary or advisable for the proper administration of the Plan. The Committee shall have the authority to interpret and make decisions
under the Plan in its sole discretion including but not limited to determining whether the Performance Goal and other conditions that are a prerequisite to earning an Award have been met and exercising discretion to reduce or eliminate the amount to
be provided as an incentive payment hereunder. Any decision or interpretation by the Committee hereunder shall be final and conclusive for all purposes and binding upon all Participants or former Participants and their successors in interest.

(c) Neither the Committee nor any member of the Committee shall be liable for any act, omission, interpretation,
construction or determination made in good faith in connection with the Plan, and the members of the Committee shall be entitled to indemnification and reimbursement by Chipotle in respect of any claim, loss, damage or expense (including, without
limitation, reasonable attorneys fees) arising or resulting therefrom to the fullest extent permitted by law.

Section 3.

Eligibility.

Awards may
be granted to officers, executive directors and key employees of the Company who are selected for participation in the Plan by the Committee. The Committee shall select in writing who shall receive an Award with respect to a Performance Period
within 90 days after the beginning of such Performance Period. A qualifying employee selected by the Committee to participate in the Plan shall be a Participant with respect to such Performance Period. Provided the Committee
determines that the Company has met the Performance Goal for the Performance Period as set forth under Section 5 below and all other eligibility requirements are met, the following guidelines will be used to determine Participants
incentive award eligibility. Awards are not guaranteed and will not be paid unless the Performance Goal is met and the Committee authorizes the payment of an incentive payment hereunder.

Each employee whose employment terminates prior to the end of a Performance Period will not be eligible to receive an incentive award
under the Plan for that Performance Period. Notwithstanding the foregoing, if a Participants employment is terminated due to retirement with Boards consent, permanent disability or death before the end of a Performance Period, the
Committee may, in its sole discretion, provide a prorated incentive award based on the number of days the Participant was employed by the Company during such Performance Period; provided, however, that no prorated incentive will be paid unless all
of the applicable requirements set forth in the Plan are met, including without limitation that the Committee determines that the Performance Goal for the applicable

Performance Period has been met and authorizes the payment of incentive awards. If the employment of a Participant terminates during a Performance Period for any other reason, no incentive award
will be paid to the Participant for that Performance Period.

Section 4.

Compliance Requirements.

A Participant must comply with all applicable state and federal regulations and Company policies (collectively, the Compliance Requirements) in order to be eligible to receive an incentive
award under the Plan. A Participant whose employment is terminated after the end of a Performance Period, but before incentive awards for such Performance Period are paid, due to violating any of the Compliance Requirements or other reasons
involving cause will not be eligible to receive an incentive award for such Performance Period.

Section 5.

Performance Goal.

The
Committee may grant performance-based awards (Awards) to Participants with respect to a Performance Period beginning on or after January 1, 2014 subject to the terms and conditions of the Plan. Each Award shall provide that
the Performance Goal is the Companys achievement of positive Operating Income (as defined below) for the then current Performance Period. For purposes of the Plan, Operating Income means, with respect to a Performance Period,
operating income as presented in Chipotles consolidated audited financial statements, excluding (i) restructuring and/or other nonrecurring charges; (ii) exchange rate effects, as applicable, for non-US dollar denominated net sales
and operating earnings; (iii) the effects of changes to generally accepted accounting standards required by the Financial Accounting Standards Board; (iv) the effects to any statutory adjustments to corporate tax rates and (v) the
impact of any extraordinary items as determined under generally accepted accounting principles. In the manner required by Section 162(m) of the Code, the Committee shall, promptly after the date on which the necessary financial and
other information for a particular Performance Period becomes available, certify whether or not the Performance Goal has been achieved.

Section 6.

Payment.

If the
Committee has determined that the Company has attained the Performance Goal for a Performance Period, the amount payable under the Award for that Performance Period shall be $8,000,000 provided, however, that the Committee may in its sole discretion
exercise discretion to reduce or eliminate the amount payable to any Participant based on such factors as the Committee may deem appropriate; including a manner consistent with corporate and individual performance as measured under Chipotles
annual performance-based cash incentive program for all of our full-time regional and corporate employees. In no event may the Committee increase the amount of any Award payable to any Participant above $8,000,000 for a Performance Period. For
purposes of clarity, the Committee may exercise the discretion provided for by the foregoing sentence in a non-uniform manner among Participants, including taking into account individual performance. Awards shall be settled in cash or, in the
Committees sole discretion, in shares of Chipotles common stock from the Amended and Restated Chipotle Mexican Grill, Inc. 2011 Stock Incentive Plan or other Chipotle equity compensation plan that has been approved by shareholders. The
Company shall pay Awards as soon as administratively practical following certification that the Performance Goal for a Performance Period has been met as provided under Section 5 above and the determination of the actual incentive amounts after
the exercise of any discretion under this Section 6, but in no event more than two and one half months following the end of the Performance Period to which such certification relates except as provided under Section 7 below.

Section 7.

Forfeiture and Recovery for Misconduct.

(a) Right of Recovery. Notwithstanding any other provision of the Plan to the contrary, if the Board (or its authorized designee) determines during the Recovery Period (as defined below) that a
Participant has engaged in Misconduct (as defined below), the Board, subject to the limitations set forth in this Section 7, may in its sole discretion

(i) terminate such Participants participation in the Plan, or with respect to any Award under the Plan, and treat any outstanding Award as forfeited

(ii) require forfeiture, in whole or in part, of payment of any Award that
has been previously approved for payment under the Plan which remains in whole or in part unpaid, and/or

(iii)
demand that the Participant pay to Chipotle in cash the amount described in Section 7(d) below; provided, however, that in the event the Board determines during the Recovery Period that the Participant engaged in Misconduct as described in
clause (iv) of the definition of Misconduct) (Restatement Misconduct), the Board shall in all circumstances, in addition to any other recovery action taken, require forfeiture and demand repayment pursuant hereto.

(i) if the Misconduct relates to Restatement Misconduct, or the Misconduct consists of acts or omissions relating to the
Companys financial matters that in the discretion of the Board are reasonably unlikely to be discovered prior to the end of the Performance Period in which the Misconduct occurred and the completion of the outside audit of the Companys
annual financial statements, the period during which the Participant is employed by the Company and the period ending two years after the Participants last day of employment,

(ii) if the Misconduct relates to the breach of any agreement between the Participant and the Company, the term of the
agreement and the period ending one year following the expiration of such agreement, and

(iii) in all other
cases, the period during which the Participant is employed by the Company and the period ending one year after the Participants last day of employment.

If during the Recovery Period the Board gives written notice to the Participant of potential Misconduct, the Recovery Period shall be extended for such reasonable time as the Board may specify is
appropriate for it to make a final determination of Misconduct and seek enforcement of any of its remedies described above. The Companys rights pursuant to this Section 7 shall terminate on the effective date of a Change in Control (as
defined in the Chipotle Mexican Grill, Inc. 2011 Stock Incentive Plan) and no Recovery Period shall extend beyond that date except with respect to any Participant for which the Board prior to such Change in Control gave written notice to such
Participant of potential Misconduct.

For purposes of administratively enforcing its rights under this Section 6, during
any period for which potential Misconduct has been identified by the Company, the Board may suspend such Participants participation in the Plan, or with respect to any Award, or temporarily withhold, in whole or in part, payment of any Award
that has been previously approved for payment that remains in whole or in part unpaid.

(c) Definition of Misconduct.

Misconduct, as determined by the Company (which determination shall be conclusive), shall mean:

(i) material breach by the Participant of any provision of any employment, consulting, advisory, proprietary information,
non-disclosure, non-competition, non-solicitation or other similar agreement between the Participant and the Company,

(ii) Violation by the Participant of the Code of Conduct,

(iii)
the Participants engagement in intentional deceitful act(s) that results in (A) an improper personal benefit, or (B) injury to Chipotle or any of its subsidiaries or affiliates; or

(iv) The Participants engagement in fraud or willful misconduct (not acting in good faith or with reasonable belief
that conduct was in the best interests of Chipotle or its subsidiaries or affiliates) that significantly contributes to Chipotle preparing a material financial restatement, other than a restatement of financial statements that became materially
inaccurate because of revisions to generally accepted accounting principles.

(d) Amount of Recovery. With respect to Misconduct described in
clause (i) of the definition of Misconduct (breach of agreement) and clause (ii) of such definition (violation of Code of Conduct), and in addition to its right to effect a termination of participation and a forfeiture of outstanding
Awards under the Plan, the Board may recover from the Participant the amount of any payments made to the Participant under the Plan during the last 12 months of employment with the Company. With respect to Misconduct described in clause
(iii) of the definition of Misconduct (intentional deceitful acts), and in addition to its right to effect a termination of participation and a forfeiture of outstanding awards under the Plan, the Board may recover from the Participant the
greater of (1) the amount paid to the Participant with respect to any Award made under the Plan with a fiscal year that includes any period during which the Misconduct occurred, or with a fiscal year which was directly impacted by the
Misconduct, or (2) the amount determined by the Board in its sole discretion to represent the financial impact of the Misconduct upon the Company; provided, however, that such recovery amount shall be reduced by the value of any forfeited
outstanding awards under the Plan (value to be reasonably determined by the Committee) and any amounts recovered from the Participant under the Companys cash bonus plans and other short term or long term incentive plans as a result of such
Misconduct. With respect to Restatement Misconduct, and in addition to its right to effect a termination of participation and a forfeiture of outstanding awards under the Plan, the Board shall seek to recover the entire amount paid to the
Participant with respect to any award made under the Plan in the twenty-four (24) month period following the first public issuance of the financial statements that are the subject of an accounting restatement relating to the Misconduct. The
term recover or recovered shall include, but shall not be limited to, any right of set-off, reduction, recoupment, off-set, forfeiture, or other attempt by Chipotle to withhold or claim payment of an award or any proceeds
thereof. Chipotles right of forfeiture and recovery of awards shall not limit any other right or remedy available to Chipotle with respect to a Participants Misconduct, whether in law or equity, including but not limited to injunctive
relief, terminating the Participants employment with Chipotle, or taking other legal action against the Participant.

The amount that may be recovered under this Section 7 shall be determined on a gross basis without reduction for taxes paid or
payable by a Participant.

Section 8.

Dodd-Frank Clawback.

Notwithstanding any other provision of the Plan to the contrary, in order to comply with Section 10D of the Securities Exchange Act
of 1934, as amended, and any regulations promulgated, or national securities exchange listing conditions adopted, with respect thereto (collectively, the Clawback Requirements), if Chipotle is required to prepare an accounting
restatement due to its material noncompliance with any financial reporting requirements under the securities laws, then the Participant shall return to Chipotle, or forfeit if not yet paid, the amount of any payment received with respect to an Award
under the Plan during the three-year period preceding the date on which Chipotle is required to prepare the accounting restatement, based on the erroneous data, in excess of what would have been paid to the Participant under the accounting
restatement as determined by the Committee in accordance with the Clawback Requirements and any policy adopted by the Committee pursuant to the Clawback Requirements.

Section 9.

General Provisions.

(a)
No Rights to Awards or Continued Employment. No employee of the Company shall have any claim or right to receive Awards under the Plan. Neither the Plan nor any action taken under the Plan shall be construed as giving any employee any right
to be retained by the Company.

(b) No Limits on Other Awards and Plans. Nothing contained in the Plan shall prohibit
the Company from establishing other special awards or compensation plans providing for the payment of compensation to employees of the Company, including any Participants.

(c) Withholding Taxes. The Company shall deduct from all payments and distributions under the Plan any required federal, state or local governments tax withholdings.

(d) Rights are Non-Assignable. A Participant nor any beneficiary nor any other person
shall have any right to assign the right to receive payments hereunder, in whole or in part, which payments are non-assignable and non-transferable, whether voluntarily or involuntarily.

(e) Unfunded Status of Plan. The Company shall not have any obligation to establish any separate fund or trust or other
segregation of assets to provide for payments under the Plan. To the extent any person acquires any rights to receive payments hereunder from the Company, such rights shall be no greater than those of an unsecured creditor.

(f) Effective Date; Amendment. The Plan shall become effective on January 1, 2014 if approved by Chipotles stockholders
at Chipotles 2013 annual stockholder meeting. The Committee may at any time and from time to time alter, amend, suspend or terminate the Plan in whole or in part; provided, however, (i) any change to the Performance Goal or (ii) any
alteration or amendment that requires shareholder approval in order to allow Awards under the Plan to qualify as performance-based compensation under Section 162(m) of the Code or to comply with other applicable laws or regulations,
shall be made subject to such shareholder approval.

(g) Governing Law. The Plan and the rights of all persons under
the Plan shall be construed and administered in accordance with the laws of the State of Delaware without regard to its conflict of law principles.

(h) Interpretation. The Plan is designed and intended to comply with the requirements for performance-based compensation under Section 162(m) of the Code and all provisions hereof
shall be construed consistent with this intention.

Approved by the Board of Directors on March 14, 2013, subject to shareholder
approval.

EX-31.1

Exhibit 31.1

CERTIFICATION

I, Steve Ells, certify that:

1. I have reviewed this quarterly report on Form 10-Q of Chipotle Mexican Grill, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under
which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial
statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrants other certifying officers and I are responsible for establishing and maintaining disclosure controls and procedures
(as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a)

Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material
information
relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b)

Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide
reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c)

Evaluated the effectiveness of the registrants disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the
disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d)

Disclosed in this report any change in the registrants internal control over financial reporting that occurred during the registrants most recent fiscal
quarter (the registrants fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrants internal control over financial reporting; and

5. The registrants other certifying officers and I have disclosed, based on our most recent evaluation of internal
control over financial reporting, to the registrants auditors and the audit committee of the registrants board of directors (or persons performing the equivalent functions):

(a)

All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely
affect the registrants ability to record, process, summarize and report financial information; and

(b)

Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrants internal control over financial
reporting.

Date: July 18, 2013

/s/ Steve Ells

Steve Ells

Founder, Chairman and Co-Chief Executive Officer

(Principal Executive Officer)

17

EX-31.2

Exhibit 31.2

CERTIFICATION

I, Montgomery F. Moran, certify that:

1. I have reviewed this quarterly report on Form 10-Q of Chipotle Mexican Grill, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under
which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial
statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrants other certifying officers and I are responsible for establishing and maintaining disclosure controls and procedures
(as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a)

Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material
information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b)

Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide
reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c)

Evaluated the effectiveness of the registrants disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the
disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d)

Disclosed in this report any change in the registrants internal control over financial reporting that occurred during the registrants most recent fiscal
quarter (the registrants fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrants internal control over financial reporting; and

5. The registrants other certifying officers and I have disclosed, based on our most recent evaluation of internal
control over financial reporting, to the registrants auditors and the audit committee of the registrants board of directors (or persons performing the equivalent functions):

(a)

All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely
affect the registrants ability to record, process, summarize and report financial information; and

(b)

Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrants internal control over financial
reporting.

Date: July 18, 2013

/s/ Montgomery F. Moran

Montgomery F. Moran

Co-Chief Executive Officer

(Principal Executive Officer)

18

EX-31.3

Exhibit 31.3

CERTIFICATION

I, John R. Hartung, certify that:

1. I have reviewed this quarterly report on Form 10-Q of Chipotle Mexican Grill, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under
which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial
statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrants other certifying officers and I are responsible for establishing and maintaining disclosure controls and procedures
(as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a)

Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material
information
relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b)

Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide
reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c)

Evaluated the effectiveness of the registrants disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the
disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d)

Disclosed in this report any change in the registrants internal control over financial reporting that occurred during the registrants most recent fiscal
quarter (the registrants fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrants internal control over financial reporting; and

5. The registrants other certifying officers and I have disclosed, based on our most recent evaluation of internal
control over financial reporting, to the registrants auditors and the audit committee of the registrants board of directors (or persons performing the equivalent functions):

(a)

All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely
affect the registrants ability to record, process, summarize and report financial information; and

(b)

Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrants internal control over financial
reporting.

Date: July 18, 2013

/s/ John R. Hartung

John R. Hartung

Chief Financial Officer

(Principal Financial Officer)

19

EX-32.1

Exhibit 32.1

CERTIFICATION PURSUANT TO

18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

In accordance with 18
U.S.C. 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, Steve Ells, the Founder, Chairman and Co-Chief Executive Officer Chipotle Mexican Grill, Inc. (the Registrant), Montgomery F. Moran, the Co-Chief
Executive Officer of the Registrant and John R. Hartung, the Chief Financial Officer of the Registrant, each hereby certifies that, to the best of his knowledge:

1. The Registrants Quarterly Report on Form 10-Q for the period ended June 30, 2013, to which this Certification is attached as Exhibit 32.1 (the Periodic Report), fully complies
with the requirements of Section 13(a) or Section 15(d) of the Securities Exchange Act of 1934, as amended; and

2.
The information contained in the Periodic Report fairly presents, in all material respects, the financial condition of the Registrant at the end of the period covered by the Periodic Report and results of operations of the Registrant for the periods
covered by the Periodic Report.